tbuckley/cabot-search huggingface dataset:
Systemic cellular viroimmunotherapy for canine high-grade gliomas
Authors: Ana Cloquell, Isidro Mateo, Stefano Gambera, Martí Pumarola, Ramon Alemany, Javier García-Castro, Ana Judith Perisé-Barrios
Journal: Journal for ImmunoTherapy of Cancer (2022)

Background Oncolytic viruses constitute a growing field of interest, both in human and veterinary oncology, given that they are particularly helpful for treating non-surgical tumors and disseminated cancer, such as high-grade gliomas. Companion dogs present malignant gliomas with biological, genetic, phenotypic, immunological, and clinical similarities to human gliomas. These features favor comparative approaches, leading to the treatment of canine oncological patients to achieve translational applications to the human clinic. The systemic administration of oncolytic viruses presents a challenge due to their limitations in effectively targeting tumors and metastases. Therefore, the aim of this study is to evaluate the safety and antitumor activity of a virotherapy used in spontaneous canine tumors. Methods Ten dogs with high-grade rostrotentorial gliomas underwent weekly systemic endovenous cellular virotherapy with dCelyvir (canine mesenchymal stem cells infected with the canine oncolytic adenovirus ICOCAV17) for 8 weeks. Efficacy was determined in seven dogs according to the Response Assessment in Veterinary Neuro-Oncology criteria considering clinical status and MRI measurements. Medical history, physical and neurological examinations, and vaccination status were evaluated prior to and during follow-up. Safety was evaluated by physical examinations and hematological and biochemical changes in peripheral blood. Immune populations were analyzed by flow cytometry in peripheral blood and by gene expression and immunohistochemistry in the tumor microenvironment. Results The treatment was well tolerated and major adverse effects were not observed. Two dogs had partial responses (76% and 86% reduction in tumor size), and 3/7 showed stable disease. ICOCAV17 was detected in peripheral blood in nine dogs, and a correlation between the ICOCAV17 particles and anti-canine adenovirus (CAV) antibodies was observed. ICOCAV17 was detected in 3/9 tumor tissues after necropsies. Regarding tumor-infiltrating lymphocytes, the dogs with disease stabilization and partial response tended to have reduced memory B-cell infiltration and increased monocyte/macrophage lineage cells. Conclusions These findings indicate that dCelyvir is safe and presents efficacy in canine rostrotentorial high-grade gliomas. These data are relevant to the ongoing phase Ib regulated human clinical trial that is administering this virotherapy to children, adolescents, and young adults with diffuse pontine glioma. Celyvir should be further explored as a treatment in veterinary and human neuro-oncology.
Serum albumin: a pharmacokinetic marker for optimizing treatment outcome of immune checkpoint blockade
Authors: Ming Zheng
Journal: Journal for ImmunoTherapy of Cancer (2022)

As we look forward to the bright future of immune checkpoint blockade (ICB) therapy, there is still lacking a pharmacokinetic marker to understand the inter-individual differences in ICB response. ICB therapy is based on IgG antibodies that share the same homeostatic pathway with serum albumin. Therefore, serum albumin level could reflect IgG catabolic rate that directly impacts the clearance of therapeutic IgG antibodies. Through interrogating a large, clinically representative pan-cancer cohort of 1,479 ICB-treated patients, this study found that higher baseline albumin levels were significantly associated with stepwise improvements in overall survival (OS), progression-free survival (PFS), and objective response rate (ORR) ( p &lt;0.001), with the variability and reproducibility confirmed in 1,000 bootstrap-resampled cohorts. Furthermore, these findings were also confirmed in most subgroups defined by patient demographics, baseline characteristics, treatments, and cancer types, even in those with low ICB-responsive cancer types and low tumor mutation burden (TMB) (TMB≤10 mut/Mb) that most of which have not been approved by the US Food and Drug Administration (FDA) for ICB therapy. In summary, this study highlights the importance of pretreatment pharmacokinetic modeling for predicting ICB treatment outcomes. Based on serum albumin—an inexpensive, non-invasive, and easily accessible biomarker of IgG pharmacokinetics, we could take a step further towards optimizing ICB therapy.
Assessment of Body Mass Index, Polygenic Risk Score, and Development of Colorectal Cancer
Authors: Xuechen Chen, Hengjing Li, Marko Mandic, Michael Hoffmeister, Hermann Brenner
Journal: JAMA Network Open (2022)

Excess weight, the prevalence of which is high and increasing in many countries, is linked to multiple adverse health outcomes, including increased colorectal cancer (CRC) risk. Better communication of health risks associated with excess weight might support efforts of prevention.To evaluate the individual and joint associations of body mass index (BMI) and polygenic risk with CRC, to assess potential interactions among them, and to quantify by how much increased polygenic risk for CRC can be offset by having a BMI within reference range.This population-based case-control study was conducted in the Rhine-Neckar region of southwest Germany, with recruitment from 2003 to 2017. Participants with both risk factor and genetic information were included for analysis. Data analysis was conducted from December 8, 2021, to February 17, 2022.BMI was calculated as self-reported weight in kilograms approximately 10 years before diagnosis or interview and current height in meters squared. A polygenic risk score (PRS) was built based on 140 CRC-related risk loci.Individual and joint associations of BMI and PRS with CRC were estimated using multiple logistic regression. Associations of excess weight with CRC were quantified by adjusted odds ratios (aORs) and genetic risk equivalents (GREs), the equivalent outcomes conveyed by defined differences in PRS percentiles.Among 9169 participants (median [IQR] age, 69 [62-76] years; 5589 [61.0%] male participants) included, 5053 had CRC and 4116 did not. BMI of 30 or greater was associated with higher odds of having CRC compared with BMI less than 25 (aOR, 1.71; 95% CI, 1.49-1.97), independent of PRS levels (P for interaction = .45). Participants with BMI of 30 or greater and a PRS in the highest tertile had higher odds of CRC compared with participants with BMI less than 25 and a PRS in the lowest tertile (aOR, 3.82; 95% CI, 3.03-4.82). The estimated association of BMI greater than 30 with CRC risk was equivalent to that of having a 41 (95% CI, 29-53)-percentile higher PRS. BMI of 30 or greater was particularly associated with stage IV CRC (aOR, 2.21; 95% CI, 1.71-2.84).These findings suggest that excess weight was associated with CRC regardless of PRS levels. The association of having a BMI within reference range may be similar to that of having a substantially lower polygenic risk for CRC.
Tissue-Based PD-L1 Expression Is the Strongest Predictor of Overall Survival Benefit From ICI in Advanced Gastroesophageal Cancer
Authors: Xinmu Zhang, Cong Ning, Haitao Zhao
Journal: JAMA Oncology (2022)

Our website uses cookies to enhance your experience. By continuing to use our site, or clicking "Continue," you are agreeing to our Cookie Policy | Continue JAMA Oncology HomeNew OnlineCurrent IssueFor Authors Podcast Publications JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry (1919-1959) JN Learning / CMESubscribeJobsInstitutions / LibrariansReprints & Permissions Terms of Use | Privacy Policy | Accessibility Statement 2023 American Medical Association. All Rights Reserved Search All JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Forum Archive JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry Input Search Term Sign In Individual Sign In Sign inCreate an Account Access through your institution Sign In Purchase Options: Buy this article Rent this article Subscribe to the JAMA Oncology journal
Tissue-Based PD-L1 Expression Is the Strongest Predictor of Overall Survival Benefit From ICI in Advanced Gastroesophageal Cancer—Reply
Authors: Harry H. Yoon, Qian Shi, Jaffer A. Ajani
Journal: JAMA Oncology (2022)

Our website uses cookies to enhance your experience. By continuing to use our site, or clicking "Continue," you are agreeing to our Cookie Policy | Continue JAMA Oncology HomeNew OnlineCurrent IssueFor Authors Podcast Publications JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry (1919-1959) JN Learning / CMESubscribeJobsInstitutions / LibrariansReprints & Permissions Terms of Use | Privacy Policy | Accessibility Statement 2023 American Medical Association. All Rights Reserved Search All JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Forum Archive JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry Input Search Term Sign In Individual Sign In Sign inCreate an Account Access through your institution Sign In Purchase Options: Buy this article Rent this article Subscribe to the JAMA Oncology journal
Reply to Danese et al.
Authors: Carlo Felix Maria Jung, Rachel Hallit, Annegret Müller-Dornieden, Mélanie Calmels, Diane Goere, Ulriikka Chaput, Marine Camus, Jean Michel Gonzalez, Marc Barthet, Jérémie Jacques, Romain Legros, Thierry Barrioz, Fabian Kück, Ali Seif Amir Hosseini, Michael Ghadimi, Steffen Kunsch, Volker Ellenrieder, Edris Wedi, Maximilien Barret
Journal: Endoscopy (2022)

See also: Endoscopic internal drainage and low negative-pressure endoscopic vacuum therapy for anastomotic leaks after oncologic upper gastrointestinal surgeryEndoscopy 2022; 54(01): 71-74DOI: 10.1055/a-1375-8151 See also: Endoscopic internal drainage versus endoscopic vacuum therapy for upper gastrointestinal leaks: what's the real deal?Endoscopy 2023; 55(01): 100-100DOI: 10.1055/a-1888-4116
Almost back to normal life again
Authors: Peter D. Siersema
Journal: Endoscopy (2022)

The past year has seen the world return to a somewhat “normal” life (albeit with some ongoing changes) since the start of the pandemic. It has been wonderful to be able to reconnect in person with colleagues from around the world again. I would like to thank you all for your immense contribution to the journal Endoscopy last year and the year to come.
Endoscopy E-Videos – recently published
Journal: Endoscopy (2022)

Comment on: Histological R0 classification after colorectal endoscopic submucosal dissection: a gold standard with feet of clayEndoscopy 2022; 54(S 02): E798-E799DOI: 10.1055/a-1816-7853 Comment on: Ecological impact of endoscopic dilatation using the bougie cap device: a low-tech innovation to reduce waste by 99 %Endoscopy 2022; 54(S 02): E824-E825DOI: 10.1055/a-1838-3860 Comment on: Endoscopic mucosal resection with a magnetic traction system: a new strategy to facilitate complete resectionEndoscopy 2022; 54(S 02): E820-E821DOI: 10.1055/a-1826-2394 Comment on: Endoscopic ultrasound-guided intra-afferent loop entero-enterostomy using a forward-viewing echoendoscope and insertion of a metal stentEndoscopy 2022; 54(S 02): E815-E817DOI: 10.1055/a-1816-7943
Endoscopic internal drainage versus endoscopic vacuum therapy for upper gastrointestinal leaks: what's the real deal?
Authors: Francesco V. Mandarino, Alberto Barchi, Lorella Fanti, Francesco Azzolini, Riccardo Rosati, Silvio Danese
Journal: Endoscopy (2022)

See also: Endoscopic internal drainage and low negative-pressure endoscopic vacuum therapy for anastomotic leaks after oncologic upper gastrointestinal surgeryEndoscopy 2022; 54(01): 71-74DOI: 10.1055/a-1375-8151 See also: Reply to Danese et al.Endoscopy 2023; 55(01): 101-101DOI: 10.1055/a-1901-8750
AI in medicine: Where are we now and where are we going?
Authors: Md Mobashir Hasan Shandhi, Jessilyn P Dunn
Journal: Cell Reports Medicine (2022)

Advancements in AI enable personalizing healthcare, for example by investigating disease origins at the genetic or molecular level, understanding intraindividual drug effects, and fusing multi-modal personal physiological, behavioral, laboratory, and clinical data to uncover new aspects of pathophysiology. Future efforts should address equity, fairness, explainability, and generalizability of AI models.
Determining asthma endotypes and outcomes: Complementing existing clinical practice with modern machine learning
Authors: Anuradha Ray, Jishnu Das, Sally E Wenzel
Journal: Cell Reports Medicine (2022)

There is unprecedented opportunity to use machine learning to integrate high-dimensional molecular data with clinical characteristics to accurately diagnose and manage disease. Asthma is a complex and heterogeneous disease and cannot be solely explained by an aberrant type 2 (T2) immune response. Available and emerging multi-omics datasets of asthma show dysregulation of different biological pathways including those linked to T2 mechanisms. While T2-directed biologics have been life changing for many patients, they have not proven effective for many others despite similar biomarker profiles. Thus, there is a great need to close this gap to understand asthma heterogeneity, which can be achieved by harnessing and integrating the rich multi-omics asthma datasets and the corresponding clinical data. This article presents a compendium of machine learning approaches that can be utilized to bridge the gap between predictive biomarkers and actual causal signatures that are validated in clinical trials to ultimately establish true asthma endotypes.
Spatial heterogeneity of infiltrating T cells in high-grade serous ovarian cancer revealed by multi-omics analysis
Authors: Bin Yang, Xiong Li, Wei Zhang, Junpeng Fan, Yong Zhou, Wenting Li, Jingjing Yin, Xiaohang Yang, Ensong Guo, Xi Li, Yu Fu, Si Liu, Dianxing Hu, Xu Qin, Yingyu Dou, Rourou Xiao, Funian Lu, Zizhuo Wang, Tianyu Qin, Wei Wang, Qinghua Zhang, Shuaicheng Li, Ding Ma, Gordon B. Mills, Gang Chen, Chaoyang Sun
Journal: Cell Reports Medicine (2022)

Tumor-infiltrating lymphocytes (TILs), especially CD8+ TILs, represent a favorable prognostic factor in high-grade serous ovarian cancer (HGSOC) and other tumor lineages. Here, we analyze the spatial heterogeneity of different TIL subtypes in HGSOC. We integrated RNA sequencing, whole-genome sequencing, bulk T cell receptor (TCR) sequencing, as well as single-cell RNA/TCR sequencing to investigate the characteristics and differential composition of TILs across different HGSOC sites. Two immune "cold" patterns in ovarian cancer are identified: (1) ovarian lesions with low infiltration of mainly dysfunctional T cells and immunosuppressive Treg cells and (2) omental lesions infiltrated with non-tumor-specific bystander cells. Exhausted CD8 T cells that are preferentially enriched in ovarian tumors exhibit evidence for expansion and cytotoxic activity. Inherent tumor immune microenvironment characteristics appear to be the main contributor to the spatial differences in TIL status. The landscape of spatial heterogeneity of TILs may inform potential strategies for therapeutic manipulation in HGSOC.
New use for an old drug: Metformin and atrial fibrillation
Authors: Manlio Vinciguerra, Ivan Olier, Sandra Ortega-Martorell, Gregory Y.H. Lip
Journal: Cell Reports Medicine (2022)

Lal and colleagues1 reported an integrative approach—combining transcriptomics, iPSCs, and epidemiological evidence—to identify and repurpose metformin, a main first-line medication for the treatment of type 2 diabetes, as an effective risk reducer for atrial fibrillation.
A robust host-response-based signature distinguishes bacterial and viral infections across diverse global populations
Authors: Aditya M. Rao, Stephen J. Popper, Sanjana Gupta, Viengmon Davong, Krista Vaidya, Anisone Chanthongthip, Sabine Dittrich, Matthew T. Robinson, Manivanh Vongsouvath, Mayfong Mayxay, Pruksa Nawtaisong, Biraj Karmacharya, Simone A. Thair, Isaac Bogoch, Timothy E. Sweeney, Paul N. Newton, Jason R. Andrews, David A. Relman, Purvesh Khatri
Journal: Cell Reports Medicine (2022)

Limited sensitivity and specificity of current diagnostics lead to the erroneous prescription of antibiotics. Host-response-based diagnostics could address these challenges. However, using 4,200 samples across 69 blood transcriptome datasets from 20 countries from patients with bacterial or viral infections representing a broad spectrum of biological, clinical, and technical heterogeneity, we show current host-response-based gene signatures have lower accuracy to distinguish intracellular bacterial infections from viral infections than extracellular bacterial infections. Using these 69 datasets, we identify an 8-gene signature to distinguish intracellular or extracellular bacterial infections from viral infections with an area under the receiver operating characteristic curve (AUROC) > 0.91 (85.9% specificity and 90.2% sensitivity). In prospective cohorts from Nepal and Laos, the 8-gene classifier distinguished bacterial infections from viral infections with an AUROC of 0.94 (87.9% specificity and 91% sensitivity). The 8-gene signature meets the target product profile proposed by the World Health Organization and others for distinguishing bacterial and viral infections.
Uncovering the molecular subtypes of triple-negative breast cancer with a noninvasive radiomic methodology
Authors: Guan-Hua Su, Yi Xiao, Yi-Zhou Jiang, Zhi-Ming Shao
Journal: Cell Reports Medicine (2022)

In this Backstory, we illustrate how a recent work from our multidisciplinary collaborative group identifies molecular subtypes of triple-negative breast cancer with a noninvasive radiomic pipeline. These findings appeared in the July 2022 issue of Cell Reports Medicine (https://www.cell.com/cell-reports-medicine/fulltext/S2666-3791(22)00230-0).
MicroRNA-dependent suppression of biological pacemaker activity induced by TBX18
Authors: Lizbeth Sanchez, Thassio Mesquita, Rui Zhang, Ke Liao, Russell Rogers, Yen-Nien Lin, Rodrigo Miguel-dos-Santos, Akbarshakh Akhmerov, Liang Li, Asma Nawaz, Kevin Holm, Eduardo Marbán, Eugenio Cingolani
Journal: Cell Reports Medicine (2022)
The quest for the missing links in fatty liver genetics: Deep learning to the rescue!
Authors: Sami Qadri, Hannele Yki-Järvinen
Journal: Cell Reports Medicine (2022)

Park, MacLean, et al. conduct an exome-wide association study of liver fat content in the Penn Medicine BioBank.1 By leveraging machine learning-assisted analysis of clinical CT scans to quantify steatosis, they uncover previously undescribed liver fat-associated genetic variants.
Arboreal origin of consonants and thus, ultimately, speech
Authors: Adriano R. Lameira
Journal: Trends in Cognitive Sciences (2022)

The world's spoken languages are universally composed of vowels and consonants, but the primate prototypical call repertoire is almost exclusively composed of vowel-like calls. What was the origin of consonant-like calls? Their prevalence across great apes suggests that an arboreal lifestyle and extractive foraging were ecological preconditions for speech evolution.
Repetitive non-typhoidal Salmonella exposure is an environmental risk factor for colon cancer and tumor growth
Authors: Daphne M. van Elsland, Janneke W. Duijster, Jilei Zhang, Virginie Stévenin, Yongguo Zhang, Lang Zha, Yinglin Xia, Eelco Franz, Jun Sun, Lapo Mughini-Gras, Jacques Neefjes
Journal: Cell Reports Medicine (2022)
Robust endoscopic image mosaicking via fusion of multimodal estimation
Authors: Liang Li, Evangelos Mazomenos, James H. Chandler, Keith L. Obstein, Pietro Valdastri, Danail Stoyanov, Francisco Vasconcelos
Journal: Medical Image Analysis (2022)

We propose an endoscopic image mosaicking algorithm that is robust to light conditioning changes, specular reflections, and feature-less scenes. These conditions are especially common in minimally invasive surgery where the light source moves with the camera to dynamically illuminate close range scenes. This makes it difficult for a single image registration method to robustly track camera motion and then generate consistent mosaics of the expanded surgical scene across different and heterogeneous environments. Instead of relying on one specialised feature extractor or image registration method, we propose to fuse different image registration algorithms according to their uncertainties, formulating the problem as affine pose graph optimisation. This allows to combine landmarks, dense intensity registration, and learning-based approaches in a single framework. To demonstrate our application we consider deep learning-based optical flow, hand-crafted features, and intensity-based registration, however, the framework is general and could take as input other sources of motion estimation, including other sensor modalities. We validate the performance of our approach on three datasets with very different characteristics to highlighting its generalisability, demonstrating the advantages of our proposed fusion framework. While each individual registration algorithm eventually fails drastically on certain surgical scenes, the fusion approach flexibly determines which algorithms to use and in which proportion to more robustly obtain consistent mosaics.
Considerations for Imaging of Malignant Pleural Mesothelioma: A Consensus Statement from the International Mesothelioma Interest Group
Authors: Sharyn I. Katz, Christopher M. Straus, Leonid Roshkovan, Kevin G. Blyth, Thomas Frauenfelder, Ritu R. Gill, Ferry Lalezari, Jeremy Erasmus, Anna K. Nowak, Victor H. Gerbaudo, Roslyn J. Francis, Samuel G. Armato
Journal: Journal of Thoracic Oncology (2022)
Pluronic® triblock copolymer-based nanoformulations for cancer therapy: A 10-year overview
Authors: Karine Cappuccio de Castro, Julia Cedran Coco, Érica Mendes dos Santos, Janaína Artem Ataide, Renata Miliani Martinez, Mônica Helena Monteiro do Nascimento, João Prata, Pedro Ricardo Martins Lopes da Fonte, Patrícia Severino, Priscila Gava Mazzola, André Rolim Baby, Eliana Barbosa Souto, Daniele Ribeiro de Araujo, André Moreni Lopes
Journal: Journal of Controlled Release (2022)